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Convolutional Networks on Graphs for Learning Molecular Fingerprints
v1v2 (latest)

Convolutional Networks on Graphs for Learning Molecular Fingerprints

30 September 2015
David Duvenaud
D. Maclaurin
J. Aguilera-Iparraguirre
Rafael Gómez-Bombarelli
Timothy D. Hirzel
Alán Aspuru-Guzik
Ryan P. Adams
    GNN
ArXiv (abs)PDFHTML

Papers citing "Convolutional Networks on Graphs for Learning Molecular Fingerprints"

50 / 1,372 papers shown
Symbiotic Message Passing Model for Transfer Learning between
  Anti-Fungal and Anti-Bacterial Domains
Symbiotic Message Passing Model for Transfer Learning between Anti-Fungal and Anti-Bacterial DomainsIEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2023
Ronen Taub
Tanya Wasserman
Y. Savir
117
0
0
14 Apr 2023
A Comprehensive Survey on Deep Graph Representation Learning
A Comprehensive Survey on Deep Graph Representation LearningNeural Networks (Neural Netw.), 2023
Wei Ju
Zheng Fang
Yiyang Gu
Zequn Liu
Qingqing Long
...
Jingyang Yuan
Yusheng Zhao
Yifan Wang
Xiao Luo
Ming Zhang
GNNAI4TS
495
258
0
11 Apr 2023
Sheaf4Rec: Sheaf Neural Networks for Graph-based Recommender Systems
Sheaf4Rec: Sheaf Neural Networks for Graph-based Recommender SystemsACM Transactions on Recommender Systems (ACM TORS), 2023
Antonio Purificato
Giulia Cassara
F. Siciliano
Pietro Lio
Fabrizio Silvestri
200
9
0
07 Apr 2023
NMR shift prediction from small data quantities
NMR shift prediction from small data quantitiesJournal of Cheminformatics (J Cheminform), 2023
Herman Rull
Markus Fischer
S. Kuhn
50
13
0
06 Apr 2023
A Survey on Graph Diffusion Models: Generative AI in Science for
  Molecule, Protein and Material
A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material
Mengchun Zhang
Maryam Qamar
Taegoo Kang
Yuna Jung
Chenshuang Zhang
Sung-Ho Bae
Chaoning Zhang
DiffMMedIm
224
59
0
04 Apr 2023
Development and Evaluation of Conformal Prediction Methods for QSAR
Development and Evaluation of Conformal Prediction Methods for QSAR
Yuting Xu
Andy Liaw
R. Sheridan
V. Svetnik
129
4
0
03 Apr 2023
Physics and Chemistry from Parsimonious Representations: Image Analysis
  via Invariant Variational Autoencoders
Physics and Chemistry from Parsimonious Representations: Image Analysis via Invariant Variational Autoencoders
Mani Valleti
Yongtao Liu
Sergei V. Kalinin
DRL
151
5
0
30 Mar 2023
Extracting real estate values of rental apartment floor plans using
  graph convolutional networks
Extracting real estate values of rental apartment floor plans using graph convolutional networksEnvironment and Planning B Urban Analytics and City Science (EPB), 2023
A. Takizawa
GNN
95
3
0
23 Mar 2023
Difficulty in chirality recognition for Transformer architectures
  learning chemical structures from string
Difficulty in chirality recognition for Transformer architectures learning chemical structures from stringNature Communications (Nat. Commun.), 2023
Yasuhiro Yoshikai
T. Mizuno
Shumpei Nemoto
Hiroyuki Kusuhara
189
30
0
21 Mar 2023
Causal Temporal Graph Convolutional Neural Networks (CTGCN)
Causal Temporal Graph Convolutional Neural Networks (CTGCN)
Abigail Langbridge
Fearghal O'Donncha
Amadou Ba
Fabio Lorenzi
Christopher Lohse
J. Ploennigs
GNN
220
2
0
16 Mar 2023
Molecular Property Prediction by Semantic-invariant Contrastive Learning
Molecular Property Prediction by Semantic-invariant Contrastive Learning
Ziqiao Zhang
Ailin Xie
Jihong Guan
Shuigeng Zhou
109
10
0
13 Mar 2023
Are More Layers Beneficial to Graph Transformers?
Are More Layers Beneficial to Graph Transformers?International Conference on Learning Representations (ICLR), 2023
Haiteng Zhao
Shuming Ma
Dongdong Zhang
Zhi-Hong Deng
Furu Wei
202
17
0
01 Mar 2023
A semantic backdoor attack against Graph Convolutional Networks
A semantic backdoor attack against Graph Convolutional NetworksNeurocomputing (Neurocomputing), 2023
Jiazhu Dai
Zhipeng Xiong
AAML
346
12
0
28 Feb 2023
Connectivity Optimized Nested Graph Networks for Crystal Structures
Connectivity Optimized Nested Graph Networks for Crystal Structures
R. Ruff
Patrick Reiser
Jan Stuhmer
Pascal Friederich
GNN
233
18
0
27 Feb 2023
GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural
  Networks
GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural NetworksThe Web Conference (WWW), 2023
Zemin Liu
Xingtong Yu
Yuan Fang
Xinming Zhang
LLMAGAI4CE
447
225
0
16 Feb 2023
GPS++: Reviving the Art of Message Passing for Molecular Property
  Prediction
GPS++: Reviving the Art of Message Passing for Molecular Property Prediction
Dominic Masters
Josef Dean
Kerstin Klaser
Zhiyi Li
Sam Maddrell-Mander
...
D. Beker
Andrew Fitzgibbon
Shenyang Huang
Ladislav Rampášek
Dominique Beaini
175
8
0
06 Feb 2023
Towards fully covariant machine learning
Towards fully covariant machine learning
Soledad Villar
D. Hogg
Weichi Yao
George A. Kevrekidis
Bernhard Schölkopf
AI4CE
319
13
0
31 Jan 2023
Exploring QSAR Models for Activity-Cliff Prediction
Exploring QSAR Models for Activity-Cliff PredictionJournal of Cheminformatics (J Cheminform), 2023
Markus Dablander
Thierry Hanser
R. Lambiotte
Garrett M. Morris
130
37
0
31 Jan 2023
Zero-One Laws of Graph Neural Networks
Zero-One Laws of Graph Neural NetworksNeural Information Processing Systems (NeurIPS), 2023
Sam Adam-Day
Theodor-Mihai Iliant
.Ismail .Ilkan Ceylan
GNNAI4CE
236
7
0
30 Jan 2023
WL meet VC
WL meet VC
Christopher Morris
Floris Geerts
Jan Tönshoff
Martin Grohe
322
32
0
26 Jan 2023
Visiting Distant Neighbors in Graph Convolutional Networks
Visiting Distant Neighbors in Graph Convolutional Networks
Ali Hashemi
H. Makse
GNN
216
1
0
26 Jan 2023
Understanding and Improving Deep Graph Neural Networks: A Probabilistic
  Graphical Model Perspective
Understanding and Improving Deep Graph Neural Networks: A Probabilistic Graphical Model Perspective
Jiayuan Chen
Xiang Zhang
Yinfei Xu
Tianli Zhao
Renjie Xie
Wei Xu
GNNBDL
134
0
0
25 Jan 2023
Event Detection in Football using Graph Convolutional Networks
Event Detection in Football using Graph Convolutional Networks
A. Rana
GNN
177
2
0
24 Jan 2023
Everything is Connected: Graph Neural Networks
Everything is Connected: Graph Neural NetworksCurrent Opinion in Structural Biology (Curr. Opin. Struct. Biol.), 2023
Petar Velickovic
GNNAI4CE
241
245
0
19 Jan 2023
State of the Art and Potentialities of Graph-level Learning
State of the Art and Potentialities of Graph-level LearningACM Computing Surveys (ACM Comput. Surv.), 2023
Zhenyu Yang
Ge Zhang
Hongzhi Zhang
Jian Yang
Quan.Z Sheng
...
Charu C. Aggarwal
Hao Peng
Wenbin Hu
Edwin R. Hancock
Pietro Lio
GNNAI4CE
263
25
0
14 Jan 2023
Faithful and Consistent Graph Neural Network Explanations with Rationale
  Alignment
Faithful and Consistent Graph Neural Network Explanations with Rationale AlignmentACM Transactions on Intelligent Systems and Technology (ACM TIST), 2023
Tianxiang Zhao
Dongsheng Luo
Xiang Zhang
Suhang Wang
316
9
0
07 Jan 2023
Machine Learning Approach to Polymerization Reaction Engineering:
  Determining Monomers Reactivity Ratios
Machine Learning Approach to Polymerization Reaction Engineering: Determining Monomers Reactivity Ratios
Tung Nguyen
Mona Bavarian
91
1
0
03 Jan 2023
EDoG: Adversarial Edge Detection For Graph Neural Networks
EDoG: Adversarial Edge Detection For Graph Neural Networks
Xiaojun Xu
Yue Yu
Hanzhang Wang
Alok Lal
C.A. Gunter
Bo Li
AAML
309
12
0
27 Dec 2022
A Generalization of ViT/MLP-Mixer to Graphs
A Generalization of ViT/MLP-Mixer to GraphsInternational Conference on Machine Learning (ICML), 2022
Xiaoxin He
Bryan Hooi
T. Laurent
Adam Perold
Yann LeCun
Xavier Bresson
243
122
0
27 Dec 2022
Multi-modal Molecule Structure-text Model for Text-based Retrieval and
  Editing
Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing
Shengchao Liu
Weili Nie
Chengpeng Wang
Jiarui Lu
Zhuoran Qiao
Ling Liu
Jian Tang
Chaowei Xiao
Anima Anandkumar
277
226
0
21 Dec 2022
A Non-Asymptotic Analysis of Oversmoothing in Graph Neural Networks
A Non-Asymptotic Analysis of Oversmoothing in Graph Neural NetworksInternational Conference on Learning Representations (ICLR), 2022
Xinyi Wu
Zhengdao Chen
W. Wang
Ali Jadbabaie
273
51
0
21 Dec 2022
MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular
  Representation Learning
MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning
Cameron Diao
Kaixiong Zhou
Zirui Liu
Xiao Huang
Helen Zhou
169
16
0
20 Dec 2022
Graph Neural Networks in Computer Vision -- Architectures, Datasets and
  Common Approaches
Graph Neural Networks in Computer Vision -- Architectures, Datasets and Common ApproachesIEEE International Joint Conference on Neural Network (IJCNN), 2022
Maciej Krzywda
S. Lukasik
Amir H. Gandomi
GNN
239
13
0
20 Dec 2022
Dynamic Molecular Graph-based Implementation for Biophysical Properties
  Prediction
Dynamic Molecular Graph-based Implementation for Biophysical Properties Prediction
C. Knutson
G. Panapitiya
R. Varikoti
Neeraj Kumar
AI4CE
192
1
0
20 Dec 2022
Graph Learning and Its Advancements on Large Language Models: A Holistic
  Survey
Graph Learning and Its Advancements on Large Language Models: A Holistic Survey
Shaopeng Wei
Yu Zhao
Xingyan Chen
Qing Li
Fuzhen Zhuang
Ji Liu
Fuji Ren
Gang Kou
AI4CE
422
6
0
17 Dec 2022
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
Machine Learning Coarse-Grained Potentials of Protein ThermodynamicsNature Communications (Nat Commun), 2022
Maciej Majewski
Adriana Pérez
Philipp Thölke
Stefan Doerr
N. Charron
T. Giorgino
B. Husic
C. Clementi
Frank Noé
Gianni De Fabritiis
AI4CE
172
100
0
14 Dec 2022
Leave Graphs Alone: Addressing Over-Squashing without Rewiring
Leave Graphs Alone: Addressing Over-Squashing without Rewiring
Adam Santoro
Ashish Vaswani
162
15
0
13 Dec 2022
Leveraging Spatio-Temporal Dependency for Skeleton-Based Action
  Recognition
Leveraging Spatio-Temporal Dependency for Skeleton-Based Action RecognitionIEEE International Conference on Computer Vision (ICCV), 2022
Junghoon Lee
Minhyeok Lee
Suhwan Cho
Sungmin Woo
Sungjun Jang
Sangyoun Lee
226
23
0
09 Dec 2022
GAUCHE: A Library for Gaussian Processes in Chemistry
GAUCHE: A Library for Gaussian Processes in ChemistryNeural Information Processing Systems (NeurIPS), 2022
Ryan-Rhys Griffiths
Leo Klarner
Henry B. Moss
Aditya Ravuri
Sang T. Truong
...
A. Lee
Bingqing Cheng
Alán Aspuru-Guzik
P. Schwaller
Jian Tang
GP
341
56
0
06 Dec 2022
Improving Molecule Properties Through 2-Stage VAE
Improving Molecule Properties Through 2-Stage VAE
Chenghui Zhou
Barnabás Póczós
DRL
157
1
0
06 Dec 2022
An open unified deep graph learning framework for discovering drug leads
An open unified deep graph learning framework for discovering drug leads
Yueming Yin
Haifeng Hu
Zhen Yang
Jitao Yang
Chun Jimmie Ye
Jiansheng Wu
W. Goh
331
1
0
06 Dec 2022
Weisfeiler and Leman Go Relational
Weisfeiler and Leman Go RelationalLOG IN (LOG IN), 2022
Pablo Barceló
Mikhail Galkin
Christopher Morris
Miguel Romero Orth
GNN
172
33
0
30 Nov 2022
On the Ability of Graph Neural Networks to Model Interactions Between
  Vertices
On the Ability of Graph Neural Networks to Model Interactions Between VerticesNeural Information Processing Systems (NeurIPS), 2022
Noam Razin
Tom Verbin
Nadav Cohen
376
17
0
29 Nov 2022
BARTSmiles: Generative Masked Language Models for Molecular
  Representations
BARTSmiles: Generative Masked Language Models for Molecular RepresentationsJournal of Chemical Information and Modeling (JCIM), 2022
Gayane Chilingaryan
Hovhannes Tamoyan
Ani Tevosyan
N. Babayan
L. Khondkaryan
Karen Hambardzumyan
Zaven Navoyan
Hrant Khachatrian
Armen Aghajanyan
SSL
199
38
0
29 Nov 2022
FakeEdge: Alleviate Dataset Shift in Link Prediction
FakeEdge: Alleviate Dataset Shift in Link PredictionLOG IN (LOG IN), 2022
Kaiwen Dong
Yijun Tian
Zhichun Guo
Yang Yang
Nitesh Chawla
362
13
0
29 Nov 2022
Revisiting Over-smoothing and Over-squashing Using Ollivier-Ricci
  Curvature
Revisiting Over-smoothing and Over-squashing Using Ollivier-Ricci CurvatureInternational Conference on Machine Learning (ICML), 2022
K. Nguyen
Hieu Nong
T. Nguyen
Nhat Ho
Khuong N. Nguyen
Vinh Phu Nguyen
281
96
0
28 Nov 2022
Beyond 1-WL with Local Ego-Network Encodings
Beyond 1-WL with Local Ego-Network Encodings
Nurudin Alvarez-Gonzalez
Andreas Kaltenbrunner
Vicencc Gómez
217
4
0
27 Nov 2022
Deep representation learning: Fundamentals, Perspectives, Applications,
  and Open Challenges
Deep representation learning: Fundamentals, Perspectives, Applications, and Open Challenges
K. T. Baghaei
Amirreza Payandeh
Pooya Fayyazsanavi
Shahram Rahimi
Zhiqian Chen
Somayeh Bakhtiari Ramezani
FaMLAI4TS
215
10
0
27 Nov 2022
Invariance-Aware Randomized Smoothing Certificates
Invariance-Aware Randomized Smoothing CertificatesNeural Information Processing Systems (NeurIPS), 2022
Jan Schuchardt
Stephan Günnemann
AAML
215
8
0
25 Nov 2022
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular
  Representation
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation
Zhen Wang
Zheng Feng
Yanjun Li
Bowen Li
Yongrui Wang
C. Sha
Min He
Xiaolin Li
AI4CE
211
11
0
25 Nov 2022
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